Since the e-ticket represents the contract of carriage and if it says 2PC for the whole itinerary, I would have thought that you were entitled to 2PC all the way. No specific experience with AF on this issue, but it seems to me that through-tickets have the same allowance throughout regardless of stopovers. It may be that non-contractual extra allowances are different (elite allowances, tolerances, etc...) but it seems to me that it would be difficult for AF to tell you that you are not entitled to what your contract of carriage says you are entitled to.